# calc_grid
#' Calculate indicators of which marker/pseudomarker positions are along a fixed grid
#'
#' Construct vectors of logical indicators that indicate which
#' positions correspond to locations along a grid
#'
#' @md
#'
#' @param map A list of numeric vectors; each vector gives marker
#' positions for a single chromosome.
#' @param step Distance between pseudomarkers and markers; if
#' `step=0` no pseudomarkers are inserted.
#' @param off_end Distance beyond terminal markers in which to insert
#' pseudomarkers.
#' @param tol Tolerance for determining whether a pseudomarker would
#' duplicate a marker position.
#'
#' @return A list of logical (TRUE/FALSE) vectors that indicate, for a
#' marker/pseudomarker map created by
#' [insert_pseudomarkers()] with `step`>0 and
#' `stepwidth="fixed"`, which positions correspond to he
#' locations along the fixed grid.
#'
#' @details The function [insert_pseudomarkers()], with
#' `stepwidth="fixed"`, will insert a grid of pseudomarkers,
#' to a marker map. The present function gives a series of
#' TRUE/FALSE vectors that indicate which positions fall on the
#' grid. This is for use with [probs_to_grid()], for
#' reducing genotype probabilities, calculated with
#' [calc_genoprob()], to just the positions on the grid.
#' The main value of this is to speed up genome scan computations
#' in the case of very dense markers, by focusing on just a grid
#' of positions rather than on all marker locations.
#'
#' @export
#' @keywords utilities
#' @seealso [insert_pseudomarkers()], [probs_to_grid()],
#' [map_to_grid()]
#'
#' @examples
#' iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
#' gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)
#' grid <- calc_grid(iron$gmap, step=1)
calc_grid <-
function(map, step=0, off_end=0, tol=0.01)
{
# is input not a map but a cross2 object?
cl <- class(map)
if(length(cl)==1 && cl=="cross2") {
map <- map$gmap
if(is.null(map))
stop("Input is a cross2 object, but no genetic map found.")
}
grid <- map
chr <- names(grid) <- names(map)
for(i in seq(along=map)) {
grid[[i]] <- calc_grid_onechr(map[[i]], step, off_end, tol,
paste0("c", chr[i], ".loc"))
}
grid
}
# grid for pseudomarkers
#
# map = vector of marker positions; names = marker names
# step = distance between pseudomarkers
# off_end = amount to go beyond the terminal markers
# tol = tolerance for determining whether a marker hits a pseudomarker
# pmar_stem = leading part of name of pseudomarkers
calc_grid_onechr <-
function(map, step=0, off_end=0, tol=0.01, pmar_stem="loc")
{
if(step==0) {
grid <- rep(TRUE, length(map))
names(grid) <- names(map)
return(grid)
}
if(any(is.na(map))) stop("map values can't be missing")
if(tol < 0) stop("tol should be >= 0")
# locations of pseudomarkers
pmar_map <- seq(min(map)-off_end, max(map)+off_end, by=step)
# for each pseudomarker, distance to nearest marker
d <- abs(outer(map, pmar_map, "-"))
mind <- apply(d, 2, min)
# omit pseudomarkers that hit a marker
to_omit <- (mind < tol)
pmar_map <- pmar_map[!to_omit]
if(length(pmar_map) == 0) {
grid <- rep(TRUE, length(map))
names(grid) <- names(map)
return(grid)
}
# markers that are on pseudomarker grid
grid <- rep(FALSE, length(map))
names(grid) <- names(map)
if(any(to_omit))
grid[apply(d[,to_omit,drop=FALSE], 2, which.min)] <- TRUE
if(is.null(names(pmar_map)))
names(pmar_map) <- create_pseudomarker_names(pmar_map, step, pmar_stem)
# logical vector indicating grid
pmar_grid <- rep(TRUE, length(pmar_map))
names(pmar_grid) <- names(pmar_map)
grid <- c(grid, pmar_grid)
# add pseudomarkers to markers
map <- c(map, pmar_map)
# sort the map
o <- order(map)
grid[o]
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.